Variant report

Variant	rs12489287
Chromosome Location	chr3:67566715-67566716
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 33 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs11919650	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11919747	0.89[EUR][1000 genomes]
rs11923127	0.84[EUR][1000 genomes]
rs11927204	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12488930	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12636825	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs17046528	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17046546	1.00[CEU][hapmap];0.81[CHB][hapmap];0.89[EUR][1000 genomes]
rs4371532	1.00[CEU][hapmap];0.93[EUR][1000 genomes]
rs4856869	0.91[EUR][1000 genomes]
rs4856872	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4856873	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4856874	1.00[CEU][hapmap];0.81[CHB][hapmap];0.87[EUR][1000 genomes]
rs4856875	0.84[EUR][1000 genomes]
rs5028414	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs56020437	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs56246741	0.87[EUR][1000 genomes]
rs56361934	0.85[EUR][1000 genomes]
rs58093651	0.89[EUR][1000 genomes]
rs61386974	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6548615	0.84[EUR][1000 genomes]
rs6768958	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6784255	0.84[EUR][1000 genomes]
rs72923195	0.89[EUR][1000 genomes]
rs72924913	0.84[EUR][1000 genomes]
rs7623441	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1007093	chr3:67113534-67602973	Weak transcription ZNF genes & repeats Enhancers Strong transcription Active TSS Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
2	nsv470638	chr3:67367341-67814738	Weak transcription ZNF genes & repeats Enhancers Active TSS Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
3	nsv460700	chr3:67393629-67712970	Genic enhancers Enhancers Flanking Active TSS Weak transcription Strong transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
4	nsv590560	chr3:67393629-67712970	Weak transcription Flanking Bivalent TSS/Enh Enhancers Active TSS Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
5	nsv834719	chr3:67396626-67589852	Strong transcription Enhancers Weak transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	2 gene(s)	inside rSNPs	diseases
6	nsv1012416	chr3:67546244-67615531	Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
7	nsv590561	chr3:67548852-67690626	Strong transcription Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:110 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:67500800-67567000	Weak transcription	Pancreas	Pancrea
2	chr3:67508200-67577600	Weak transcription	Spleen	Spleen
3	chr3:67513400-67567800	Weak transcription	NHLF	lung
4	chr3:67521600-67580400	Weak transcription	Stomach Mucosa	stomach
5	chr3:67524200-67567000	Weak transcription	Placenta	Placenta
6	chr3:67526800-67583200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr3:67531400-67576200	Weak transcription	HMEC	breast
8	chr3:67533200-67577000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
9	chr3:67533400-67577600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
10	chr3:67534400-67576400	Weak transcription	Aorta	Aorta
11	chr3:67535000-67578800	Weak transcription	Brain Hippocampus Middle	brain
12	chr3:67537400-67579600	Weak transcription	Small Intestine	intestine
13	chr3:67537600-67566800	Weak transcription	Duodenum Smooth Muscle	Duodenum
14	chr3:67541400-67582000	Weak transcription	Rectal Smooth Muscle	rectum
15	chr3:67544200-67580200	Weak transcription	Placenta Amnion	Placenta Amnion
16	chr3:67544400-67567200	Weak transcription	Fetal Muscle Trunk	muscle
17	chr3:67544800-67577600	Weak transcription	Thymus	Thymus
18	chr3:67552000-67566800	Weak transcription	HepG2	liver
19	chr3:67553800-67579600	Weak transcription	Hela-S3	cervix
20	chr3:67554600-67577800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
21	chr3:67555800-67567800	Weak transcription	Fetal Muscle Leg	muscle
22	chr3:67555800-67579600	Weak transcription	Brain Cingulate Gyrus	brain
23	chr3:67557400-67583200	Weak transcription	K562	blood
24	chr3:67558400-67571400	Strong transcription	Primary B cells from peripheral blood	blood
25	chr3:67558400-67580200	Weak transcription	Fetal Thymus	thymus
26	chr3:67558800-67567000	Weak transcription	Primary hematopoietic stem cells	blood
27	chr3:67559600-67577600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
28	chr3:67560200-67581800	Weak transcription	Colon Smooth Muscle	Colon
29	chr3:67560400-67577600	Weak transcription	Right Ventricle	heart
30	chr3:67560600-67567000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
31	chr3:67560600-67567000	Weak transcription	Skeletal Muscle Male	skeletal muscle
32	chr3:67560600-67567000	Weak transcription	NHEK	skin
33	chr3:67560600-67576800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
34	chr3:67560600-67580200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
35	chr3:67560600-67586200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
36	chr3:67560600-67620800	Weak transcription	Esophagus	oesophagus
37	chr3:67561800-67579400	Strong transcription	Primary T helper cells fromperipheralblood	blood
38	chr3:67563400-67571800	Strong transcription	Primary T helper cells PMA-I stimulated	--
39	chr3:67563400-67571800	Strong transcription	Rectal Mucosa Donor 29	rectum
40	chr3:67563400-67572000	Strong transcription	Primary T cells from cord blood	blood
41	chr3:67563600-67567200	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
42	chr3:67563600-67567800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
43	chr3:67563600-67568000	Strong transcription	GM12878-XiMat	blood
44	chr3:67563800-67567200	Strong transcription	Duodenum Mucosa	Duodenum
45	chr3:67563800-67568200	Strong transcription	Sigmoid Colon	Sigmoid Colon
46	chr3:67563800-67569800	Strong transcription	Ovary	ovary
47	chr3:67563800-67571200	Strong transcription	Dnd41	blood
48	chr3:67563800-67571400	Strong transcription	Primary B cells from cord blood	blood
49	chr3:67563800-67571800	Strong transcription	Monocytes-CD14+_RO01746	blood
50	chr3:67563800-67572200	Strong transcription	Primary T cells fromperipheralblood	blood

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